8QEQ | pdb_00008qeq

RNA polymerase II bound to minimal Alu RNA right arm in the alternative conformation

• PDB DOI: https://doi.org/10.2210/pdb8QEQ/pdb
• EM Map EMD-18376: EMDB EMDataResource
• NAKB: 8QEQ

• Classification: TRANSCRIPTION
• Organism(s): Sus scrofa domesticus, Homo sapiens
• Mutation(s): No 


• Deposited: 2023-09-01 Released: 2024-12-11 
• Deposition Author(s): Tluckova, K., Bernecky, C.
• Funding Organization(s): Austrian Science Fund

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Mechanism of mammalian transcriptional repression by noncoding RNA.

Tluckova, K., Kaczmarek, B., Salmazo, A., Bernecky, C.

(2025) Nat Struct Mol Biol 32: 607-612

• PubMed: 39762629 
• DOI: https://doi.org/10.1038/s41594-024-01448-7
• Primary Citation of Related Structures:  
  8QEP, 8QEQ


• PubMed Abstract: 
  

  Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.

---

Organizational Affiliation: 
• Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A1B1C1D1E1F1G1H1I1J1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 506.99 kDa 
• Atom Count: 29,242 
• Modeled Residue Count: 3,605 
• Deposited Residue Count: 4,349 
• Unique protein chains: 10
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	A	1,970	Sus scrofa domesticus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa) Explore A0A8D1DPV6  Go to UniProtKB:  A0A8D1DPV6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,174	Sus scrofa domesticus	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus) Explore A0A0B8RVL1  Go to UniProtKB:  A0A0B8RVL1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	275	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3  Go to UniProtKB:  I3LCH3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	D [auth E]	210	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7  Go to UniProtKB:  I3LSI7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	E [auth F]	127	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9  Go to UniProtKB:  A0A4X1VEK9

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	F [auth H]	150	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2  Go to UniProtKB:  I3LCB2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	G [auth I]	125	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899  Go to UniProtKB:  P60899

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	H [auth J]	67	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa) Explore A0A8W4F9W9  Go to UniProtKB:  A0A8W4F9W9

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11-a	I [auth K]	117	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4  Go to UniProtKB:  F1RKE4

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II, I and III subunit K	J [auth L]	58	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6  Go to UniProtKB:  A0A4X1TRS6

Entity ID: 11
Molecule	Chains	Length	Organism	Image
Alu RNA Minimal Right Arm	K [auth R]	76	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	L [auth A], M [auth A], O [auth B], P [auth I], Q [auth I], R [auth J], S [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Tluckova, K., Bernecky, C.

---

Funding Organization	Location	Grant Number
Austrian Science Fund	Austria	P34185

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-01-15
  Changes: Data collection, Database references
• Version 1.2: 2025-01-22
  Changes: Data collection, Database references, Experimental preparation, Source and taxonomy, Structure summary
• Version 1.3: 2025-04-23
  Changes: Data collection, Database references